Soil microbial toxicity is an important topic for understanding the environmental risk of cerium oxide nanoparticles (nanoceria). Biolog Ecoplate, a technique that analyzes microbial functional diversity based on carbon source use, was employed to investigate microbial community profile and co-occurrence in soils planted with bokchoy (Brassica rapa subsp. chinensis) and treated with either nanoceria (NC) or cerium (III) nitrate (IC). The results showed that NC and 500 mg/kg IC treatments promoted functional diversity and microbial carbon utilizations (e.g., polysaccharides, fatty acids and lipids, amino acids) compared to other treatments. NC promoted microbial activity in 19 carbon sources (e.g., α-D-lactose, β-methyl-D-glucoside, D-xylose, N-acetyl-D-glucosamine, glucose-1-phosphate, 2-hydroxybenzoic acid, γ-hydroxybutyric acid, itaconic acid, D-malic acid, L-arginine, L-phenylalanine, L-threonine, glycyl-L-glutamic acid and phenylethylamine). The co-occurrence network analysis suggests a less compact and more responsive network for NC than IC treatments, implying that soil microbial community was more physiologically responsive to NC rather than IC. Also, correlation analysis of bacterial genera revealed that nanoceria could promote activity of soil microbes, particularly those belonging to the Proteobacteria taxa, which makes it a potential bioindicator for NC contamination.